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		<h1><a href="UCSCBin.html">UCSCBin</a></h1>
<table>
<tr><td valign="top">Author:</td><td>Hiroyuki Mishima (missy at be.to / hmishima at nagasaki-u.ac.jp)

</td></tr>
<tr><td valign="top">Copyright:</td><td>Hiroyuki Mishima, 2010

</td></tr>
<tr><td valign="top">License:</td><td>the MIT/X11 license. See the LICENSE file.

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<p>
A library for handling BIN index and 0/1-based coordination of UCSC
Bioinformatics Genome Browser ( <a
href="http://genome.ucsc.edu/">genome.ucsc.edu/</a> )
</p>
<p>
Original program in C by Jim Kent, 2002
</p>
<p>
See also related materials:
</p>
<ul>
<li><a
href="http://genomewiki.ucsc.edu/index.php/Bin_indexing_system">genomewiki.ucsc.edu/index.php/Bin_indexing_system</a>,

</li>
<li>Kent, et. al. Genome Research 2002.12:996-1006, <a
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186604/">www.ncbi.nlm.nih.gov/pmc/articles/PMC186604/</a>

</li>
<li>src/lib/binRange.c in the kent source tree. <a
href="http://hgdownload.cse.ucsc.edu/admin/jksrc.zip">hgdownload.cse.ucsc.edu/admin/jksrc.zip</a>

</li>
</ul>
<h2>UCSCBin::Util</h2>
<p>
convert between 0-based half-open interval and 1-based full-close
intervals.
</p>
<h2><a href="UCSCBin/BinRange.html">UCSCBin::BinRange</a></h2>
<p>
Calculate Bin number from genomic physical position according to
UCSC&#8217;s Bin Indexing System. note: Extended bin index for positions >=
512M is not supported yet. Do you need it? Please email the author.
</p>
<h2>sample/refseqgene.rb</h2>
<p>
to run the sample (input interval is regular 1-based full-closed
cordination)
</p>
<pre>
 sudo gem install sequel
 sample/refseqgene.rb chr1:234567-456789
</pre>
<p>
output:
</p>
<pre>
 chr1:234567-345678      LOC100133331; LOC100132287; LOC100132062
</pre>
<h2>Note on Patches/Pull Requests</h2>
<ul>
<li>github repository is git://github.com/misshie/UCSCBin.git

</li>
<li>Fork the project.

</li>
<li>Make your feature addition or bug fix.

</li>
<li>Add tests for it. This is important so I don&#8217;t break it in a future
version unintentionally.

</li>
<li>Commit, do not mess with rakefile, version, or history. (if you want to
have your own version, that is fine but bump version in a commit by itself
I can ignore when I pull)

</li>
<li>Send me a pull request. Bonus points for topic branches.

</li>
</ul>
<h2>Copyright</h2>
<p>
Copyright &#169; 2010 Hiroyuki MISHIMA. See LICENSE for details.
</p>

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